Showing papers by "Stephen E. Williams published in 2019"

Impacts of recent climate change on terrestrial flora and fauna: Some emerging Australian examples

Abstract: The effects of anthropogenic climate change on biodiversity are well known for some high‐profile Australian marine systems, including coral bleaching and kelp forest devastation. Less well‐published are the impacts of climate change being observed in terrestrial ecosystems, although ecological models have predicted substantial changes are likely. Detecting and attributing terrestrial changes to anthropogenic factors is difficult due to the ecological importance of extreme conditions, the noisy nature of short‐term data collected with limited resources, and complexities introduced by biotic interactions. Here, we provide a suite of case studies that have considered possible impacts of anthropogenic climate change on Australian terrestrial systems. Our intention is to provide a diverse collection of stories illustrating how Australian flora and fauna are likely responding to direct and indirect effects of anthropogenic climate change. We aim to raise awareness rather than be comprehensive. We include case studies covering canopy dieback in forests, compositional shifts in vegetation, positive feedbacks between climate, vegetation and disturbance regimes, local extinctions in plants, size changes in birds, phenological shifts in reproduction and shifting biotic interactions that threaten communities and endangered species. Some of these changes are direct and clear cut, others are indirect and less clearly connected to climate change; however, all are important in providing insights into the future state of terrestrial ecosystems. We also highlight some of the management issues relevant to conserving terrestrial communities and ecosystems in the face of anthropogenic climate change.

Detection and assembly of novel sequence insertions using Linked-Read technology

Abstract: Emerging Linked-Read (aka read-cloud) technologies such as the 10x Genomics Chromium system have great potential for accurate detection and phasing of large-scale human genome structural variations (SVs). By leveraging the long-range information encoded in Linked-Read sequencing, computational techniques are able to detect and characterize complex structural variations that are previously undetectable by short-read methods. However, there is no available Linked-Read method for detection and assembly of novel sequence insertions, DNA sequences present in a given sequenced sample but missing in the reference genome, without requiring whole genome de novo assembly. In this paper, we propose a novel integrated alignment-based and local-assembly-based algorithm, Novel-X, that effectively uses the barcode information encoded in Linked-Read sequencing datasets to improve detection of such events without the need of whole genome de novo assembly. We evaluated our method on two haploid human genomes, CHM1 and CHM13, sequenced on the 10x Genomics Chromium system. These genomes have been also characterized with high coverage PacBio long-reads recently. We also tested our method on NA12878, the well-known HapMap CEPH diploid genome and the child genome in a Yoruba trio (NA19240) which was recently studied on multiple sequencing platforms. Detecting insertion events is very challenging using short reads and the only viable available solution is by long-read sequencing (e.g. PabBio or ONT). Our experiments, however, show that Novel-X finds many insertions that cannot be found by state of the art tools using short-read sequencing data but present in PacBio data. Since Linked-Read sequencing is significantly cheaper than long-read sequencing, our method using Linked-Reads enables routine large-scale screenings of sequenced genomes for novel sequence insertions.